I would like to agree to what TOS said above, but I will mention that each LFS (including big box stores) are very different. It all depends on the staff.
I have a local independent LFS run by an "old school" fishkeeper. I chatted the owner up a bit regarding the fish and found out quite quickly that this guy really didn't have the fish in proper conditions. He has a HUGE bichir in a tank just barely big enough for it to turn around. His tanks always have a ton of algae growth. There's always at least one tank (usually more) that has dead or dying fish in it. His business is thriving, but I don't think that he keeps his fish very well.
Another independent near me was the one that my dad used to use for fish. I remember going there as a kid and marveling at all the tanks. There were so many fish, and so many tanks. It was awesome. I dreamed of working in a store like that some day. Then, when I got back into fishkeeping and went there - 15 years having past. It looked like I remembered, except that it showed the 15 years of decay. The store was falling down around me as I walked through. It was depressing. Sick and dying fish everywhere I looked. It was bare in some places. It was obvious this guy was going out of business and fast.
Contrast that with my local Petsmart. I went there to look at the tank I ended up purchasing. It was the size I wanted, and the dimensions fit my space perfectly. While looking at it, the fish department manager came over. We talked for about 90 minutes (I think my wife started to get jealous!

) about all things fish related. We discussed fishless cycling, which he had never done but had been curious about it. (He just clones his filters now from his old media and claims that he's had fish since he was a kid.) Then we talked about stocking. We discussed everything from neon tetra to tiger barbs all the way through African cichlids. Every bit of advice he gave on each fish was dead on with my own research, but I was probing him for information, trying to find out if he would sell me any fish I wanted. He even went so far as to suggest that I wait to add the neons because they can be a bit sensitive to new tanks, not just uncycled tanks.

(A LFS suggesting NOT to buy a fish immediately and bang it into a tank, especially one that was already cycled?!) Anyway, I have made this
my LFS. Every time I go in, the tanks are clean, the fish are active and the staff is friendly. Granted, there are different workers there, some having more information to share than others. But, the manager actually understands fish keeping, and it was evident from talking to another of the employees that he actually is training them on proper fish keeping techniques as well. One of them actually mentioned to me the one time that they didn't know the answer to a question because they just started working there and hadn't been fully trained by the manager yet.
I think blanket statements like "avoid big box stores" denies the reality that there is no perfect way to find a good LFS without visiting a bunch and talking to the staff. You can find out pretty quick how much they really know about fishkeeping and if their methods match your own.